MatrixeQTL is a classic and convenient eQTL analysis software that can be used for identifying the cis-eQTL or trans-eQTL.
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FastQTL is a fast, flexible and user-friendly QTL mapping tool.
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QTLtools is used to identify cis-QTLs, discover and analyze other molecular QTLs.
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GenomicTools can perform QTL and eQTL analysis in a user-friendly manner.
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ASE-TIGAR is software to estimate the allele-specific expression (ASE) from RNA-Seq data with diploid genomes.
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RBP-Var is applied to the annotation of functional variants which potentially influence RNA-protein interactions by changing RNA structure
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eCAVIAR can identify the target gene and the most relevant organization for a GWAS risk site, and explain the uncertainty of LD.
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SMR is a mendelian randomization tool based on summary data to identify pleiotropic genes.
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XGR is used for the enrichment, similarity, network or annotation analysis of genes, SNPS or genomic regions to enhance downstream biological discovery.
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OmicKriging is used to predict complex traits through correlation matrix.
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OmicCircos can visualize genomic variations.
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GTEx is an eQTL database of 49 healthy tissues.
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PancanQTL is a database of cis- and trans-eQTLs in different cancer types, which also contains survival-associated eQTLs and eQTLs in GWAS linkage disequilibrium (LD) regions.
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eQTLGen is a large-scale database of cis and trans eQTLs in blood tissues.
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Blood eQTL Browser is a blood-specific eQTL database with a large number of trans-eQTLs.
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EyeGEx is an eQTL database of retinal locations, filling the gap in GTEx without ocular tissue.
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SeeQTL is a searchable database for human eQTLs.
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SCAN is a large database of genetics and genomics data with eQTL annotations.
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ncRNA-eQTL is an eQTL database evaluating the effect of SNPs on ncRNA expression.
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JAMIR-eQTL is A Japanese-specific database of genetic variants affecting comprehensive serum miRNA expression.
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ImmuNexUT is the largest eQTL database in East Asia.
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Braineac is A database of eQTLs associated with neurological diseases.
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